Probit-based models relating a proportional response variable to a temporal explanatory variable, assuming that the times to response are normally distributed within the population, have been used in seed biology for describing the rate of loss of viability during seed ageing and the progress of germination over time in response to environmental signals (e.g. water, temperature). These models may be expressed as generalized linear models (GLMs) with a probit (cumulative normal distribution) link function, and, using GLM fitting procedures in current statistical software, parameters of these models are efficiently estimated while taking into account the binomial error distribution of the dependent variable. The fitted parameters can then be used to calculate the ‘traditional’ model parameters, such as the hydro- or hydrothermal time constant, the mean or median response of the seeds (e.g. mean time to death, median base water potential), and the standard deviation of the normal distribution of that response. Furthermore, through consideration of the deviance and residuals, performing model evaluation and modification can lead to improved understanding of the underlying physiological/ecological processes. However, fitting a binomial GLM is not appropriate for the cumulative count data often collected from germination studies, as successive observations are not independent, and time-to-event/survival analysis should be considered instead. This review discusses well-known probit-based models, providing advice on how to collect appropriate data and fit the models to those data, and gives an overview of alternative analysis approaches to improve understanding of the underlying mechanisms of seed dormancy and germination behaviour.

Phenotypic plasticity in seed dormancy may allow plant species to cope with rapid environmental changes, such as climate warming. In controlled experimental settings, plasticity in dormancy has been found to relate to temperature during seed maturation, but this relationship has not been tested in field conditions. Here we analyse for the first time the variation in dormancy during five successive years in wild populations of the study species Centaurium somedanum, to determine how this variation is related to average temperatures during specific seasons of plant activity. We performed laboratory germination experiments to measure: (1) the degree of dormancy at dispersal; and (2) the sensitivity to dormancy-breaking factors. We calculated average temperatures during four seasons of plant activity (overwintering, vegetative growth, flowering and seed maturation) for each year, and tested the relationship between these temperatures and patterns of dormancy variation, using Generalized Linear Models. Dormancy varied among sites and years, seeds being more dormant in colder years. For the degree of dormancy at dispersal, we found a positive relationship with flowering temperature and a significant effect of collection site. For the sensitivity to dormancy-breaking factors, we found no significant differences among sites, a positive relationship with flowering temperature and a negative relationship with overwintering temperature. Phenotypic plasticity in dormancy in C. somedanum is thus especially marked in the sensitivity to dormancy-breaking factors. Temperatures during overwintering and flowering have differential effects on this plasticity, allowing the plant to detect the gradient of seasonality, a main ecological feature of its distribution. These results highlight the importance of taking into account more than average temperatures when assessing the response of plant phenotypic plasticity to climate change.

Fluctuating temperatures terminate seed dormancy in many species, including Cynara cardunculus (L.) var. sylvestris. Termination of physiological dormancy requires low ratios of abscisic acid (ABA)/gibberellins (GA). In a previous paper we have shown that physiological responses to fluctuating temperatures comprise a reduction of abscisic acid (ABA) content and sensitivity. However, a possible stimulation of GA synthesis was also suggested as part of the mechanism. That possible stimulation, as well as the identification of potential regulatory sites for ABA and GA metabolism and signalling involved in the termination of dormancy by fluctuating temperatures, are yet to be determined. In this study, we measured GA content and sensitivity in seeds incubated under constant and fluctuating temperatures. We also assessed the expression of several genes involved in ABA and GA metabolism and signalling. Our results show that fluctuating temperatures reduce ABA/GA ratios through a reduction in ABA accumulation during incubation but without altering GA synthesis as compared to that observed under constant temperatures. On the other hand, fluctuating temperatures did not increase sensitivity to GA. Fluctuating temperatures reduced the expression of CycaNCED and CycaABI5 (ABA synthesis and signalling genes) with a temporal pattern that coincides with the interruption of ABA accumulation that precedes germination of seeds incubated under fluctuating temperatures. However, fluctuating temperatures did not modify the expression of CycaCYP707A2 (ABA inactivation) as compared to that observed under constant temperatures. Consistent with our determinations of GA content and sensitivity, fluctuating temperatures did not modify the expression of GA synthesis (CycaGA3ox) and signalling genes (CycaRGL2 and CycaGAI) in relation to that observed at constant temperatures. These results show that fluctuating temperatures terminate dormancy in Cynara cardunculus seeds through an interruption in ABA accumulation and a reduction in ABA signalling exerted at the level of CycaNCED and CycaABI5 expression.

Seed germination is regulated in a concerted manner that involves generating growth potential in the embryo to overcome the mechanical resistance of the endosperm. The wake-up call of a dry seed includes the reorganization of subcellular structures and the reactivation of metabolism in a dense, oxygen-poor environment. Pools of unbound metabolites and solutes produced by the degradation of storage reserves, including starch, proteins and oils, in the embryo can contribute to the generation of the embryo growth potential and radicle protrusion. Recent genomics studies have contributed a vast amount of data on protein, metabolite and gene transcript profiles during germination, which can be integrated to explore the seed metabolism from water imbibition to radicle protrusion. To what extent are free pools of metabolites relevant to the reorganization of seed metabolism? How is energy built to support embryo growth and radicle protrusion? Elucidating these fundamental questions in seed biology is the key to the understanding of the germination process. Here we have attempted to summarize the recent scientific knowledge to provide a comprehensive description of the ignition, reassembling and regulation of metabolism during seed germination.

Palm diaspores are reported to have various kinds of dormancy. However, (1) the embryo is underdeveloped; (2) the endocarp is water permeable; and (3) the diaspores take a long time to germinate. Thus, we conclude that the diaspores of the majority of palm species have morphophysiological dormancy (MPD). The ones that do not have MPD are morphologically dormant.

Seeds with epicotyl dormancy reside in soil up to 15 months (or longer), being exposed to a sequence of temperatures, before seedlings completely emerge (i.e. with both roots and shoots). Heretofore, few studies have examined precise temperatures, especially in sequences, for promotion of radicle and cotyledon emergence and how they relate to environmental cues in nature. Viburnum is the best known genus to exhibit epicotyl dormancy and, as such, we investigated the Japanese V.furcatum, hypothesizing a similar kind and level of dormancy. The underdeveloped embryos in mature seeds in October were spatulate shaped, unlike those in other Viburnum species, and they elongated from late June to August of the following year. Radicles emerged after embryo growth until mid-October, followed by cotyledons from mid-April to mid-May. Temperatures required for embryo growth, radicle and cotyledon emergence in the laboratory approximated closely those in the field. Embryo elongation and radicle emergence occurred at warm temperature regimes, and gibberellic acid (GA3) did not substitute for this warm temperature requirements. Following a 120-d cold stratification of seeds with an emerged radicle, shoots emerged from seeds at 10, 15, 15/5, 20/10 and 25/15°C. We identified that seeds of V. furcatum have deep simple epicotyl morphophysiological dormancy like the majority of other Viburnum species. For propagation of the species from seeds, the nearly 2-year period for seedling emergence could be shortened to 8 months: start fresh seeds at 25/15°C (60 d) and then move them through a sequence of 15/5°C (30 d) →  0°C (120 d) →  20/10°C (30 d).

Successful remobilization of seed reserves is the driving force behind seedling establishment for maximum final crop outcomes. The remobilization of stored maize seed phosphorus (P), and its allocation towards growing seedlings is critical for P-autotrophy during early ontogeny. We aimed to (1) evaluate the time frame of the origin of P utilized by maize seedlings, including the heterotrophic, transitional and autotrophic phases; and (2) compare P and carbon (C) dynamics in both seed and seedling compartments during the same phases. Using isotopic signatures (32P), we identified different P fluxes (P-heterotrophy, P-transition and P-autotrophy) and determined the proportion of P fluxes from heterotrophic seed P and external P uptake during 23 d of early ontogeny. The P-heterotrophic growth phase lasted from the first to the fourth day after sowing, when seedlings were entirely made up of heterotrophic P originating from remobilized seed P pool. In our experimental conditions, the P-transitional phase, when growing seedlings were supported by both heterotrophic and autotrophic P, lasted from the fifth to the fifteenth day after sowing. Thereafter, seed P reserves were exhausted and seedlings depended entirely on external P uptake, indicating the P-autotrophic stage. Although seed P reserves were remobilized earlier than C reserves, the length of the three growth phases for P and C was similar in the maize seedlings.

Hydration memory is a phenomenon in which a seed can tolerate discontinuous hydration periods, displaying enhanced germination after one or multiple hydration–dehydration (HD) cycles; it was described physiologically in a few cactus species around 15 years ago. Although no additional work was done on this subject, it has great biotechnological potential since its analysis would permit predictions about whether a seed can withstand discontinuous hydration; in the long run, the knowledge about its regulation might lead to induction of this resistance, so we aimed to provide an initial approach to the molecular mechanisms that underlie hydration memory. This phenomenon was reproduced successfully in our lab with Ferocactus peninsulae seeds. Using two-dimensional (2D) electrophoresis, we compared expression patterns of proteins involved in seed maturation of seeds and seedlings subjected to an HD cycle treatment. We found differential expression of several proteins possibly involved in primary metabolism, ubiquitination pathway and reserve protein availability regulation in seeds and seedlings subjected to an HD cycle. We also found differential stability of total RNA. These results strongly suggest that the differential expression of proteins is at least partially related to the hydration memory process.

We isolated two cDNAs of phosphoenolpyruvate carboxylase (PEPC) from developing rice seeds, Osppc1 and Osppc3. The deduced amino acid sequences of both cDNAs share several conserved motifs with other non-photosynthetic PEPCases, and these common motifs are known to be functionally important to their regulatory properties. The deduced protein sequence of Osppc1 was clustered into a monocotyledonous plant-specific clade, and Osppc3 was clustered into a gramineous plant-specific clade in the phylogenetic tree of plant PEPCases. The mRNA accumulations of Osppc1 and Osppc3 were found in developing rice seeds throughout the grain-filling stages, although their expression patterns differed: Osppc1 was strongly expressed at 7 d after flowering, and Osppc3 was strongly expressed at 4 d after flowering. The kinetic properties of the Osppc1 recombinant protein were quite similar to those of maize root-type PEPCase, except that the sensitivity for malate at pH 7.3 was weaker. Mining rice microarray data, we observed that Osppc1 was co-expressed with aspartate aminotransferase and alanine aminotransferase, which are involved in seed nitrogen metabolism. Moreover, reannotation of the co-expressed genes revealed that Osppc1, the two aminotransferases and the enolase were mapped on to the consecutive reaction from 2-phosphoglycerate to glutamate and pyruvate in the cytosol. These results imply that Osppc1 functions cooperatively with the two aminotransferases in the synthesis of amino acids that are used for storage protein synthesis in developing rice seeds.

Several studies have compared seed banks of the different morphs of heteromorphic species, but none of them was on an amphi-basicarpic species. Our primary aim was to compare the relative ability of aerial and basal diaspores of an amphi-basicarpic species to form a seed bank. We compared the seed-bank dynamics of basal and aerial diaspores of three populations of the cold-desert annual Ceratocarpus arenarius growing in the Junggar Desert in north-western China. A 2.5-year experimental garden study compared germination phenology and retention of viability in basal (a) and aerial (c and f) morphs. Aerial morphs formed a modified Thompson and Grime type III seed bank (small proportion of seeds carried over to next year) and the basal morph a modified type IV seed bank (large proportion of seeds carried over to next year). Seeds germinated only in spring, and cumulative germination percentages were f>c>a (year 1), f = c>a (year 2) and f = c = a (year 3). The relationship between length of germination period, retention of viability during burial and relative ability to form a persistent seed bank was basal morph > aerial morphs. The results of this seed-bank study on C. arenarius are in full agreement with those published previously on seed dispersal and dormancy in this species. Thus, strong additional support is provided for a high risk–low risk germination strategy in this cold-desert annual.

Plastochromanol-8 and tocopherols are natural antioxidants with vitamin E activity that protect seeds and plants from oxidative damage. Whereas α-tocopherol is predominant in photosynthetic tissues, γ-tocopherol is more abundant in seeds. Ethiopian mustard (Brassica carinata A. Braun) seeds contain varying levels of both tocopherol forms. The objective of this research was to study changes in plastochromanol-8 and tocopherol contents during seed germination in Ethiopian mustard lines with contrasting seed tocopherol levels, and to evaluate their influence on seed germination and seedling growth. Cotyledons and radicles of seven lines with contrasting seed tocopherol levels and a control line were sampled periodically until 120 h after sowing (HAS) under light and dark conditions, and were analysed for plastochromanol-8 and tocopherol contents. The main factors genotype, tissue, light and HAS were significant for all the traits, excepting the light effect for total tocopherol content. Most of the lines showed a gradual decrease in γ-tocopherol that was nearly completely replaced by α-tocopherol at 120 HAS. However, line BCT-4, with high γ-tocopherol content in seeds, exhibited unusually high γ-tocopherol content in cotyledons and radicles during the whole sampling period. Light treatment and initial seed tocopherol levels had no influence on germination percentage. Despite significant differences for seedling development among genotypes, no clear association between seedling development and seed tocopherols was observed. The results revealed that the unusual presence of high γ-tocopherol levels in cotyledons and radicles of line BCT-4 did not have an effect on seedling growth.

Temperature is a significant factor influencing seed germination and for many species temperature-mediated germination cues are vital for plant persistence. Rising temperatures forecast as a result of anthropogenic climate change may have a substantial influence on the population and range dynamics of plant species. Here, we report on the thermal constraints on seed germination in natural populations of four congeneric Banksia species collected from a longitudinal climate gradient in Western Australia. We investigated whether germination niche: (1) varied between species; (2) varied among populations of each species; and (3) varied in a consistent manner reflecting the climatic gradients of seed origin. We hypothesized that species would differ and that populations from warmer sites would have a broader temperature window for germination than populations from cooler sites. Species differed in the breadth of their germination niche, but temperatures that stimulated the most rapid and complete germination were similar across all species. A sharp reduction in germination percentage occurred above the optimum temperature, which coincided with significant delays in germination relative to the optimum. The temperatures causing these declines varied among populations. Across the species, there was a significant correlation between optimum germination temperature and mean annual temperature at seed source; however, there was no relationship at the population level for individual species. These data provide insight into the vulnerability of Banksia species to climate change, with those populations that require lower temperatures for germination, or have narrower optimal ranges for germination, likely to be most vulnerable to a warming climate.

Seeds can synchronize their germination and dormancy cycles to regular seasonal environmental changes. The present work sought to evaluate the in-situ longevity of the buried seeds of two species of Syngonanthus and two species of Comanthera (Eriocaulaceae) in the region of natural occurrence (Serra do Cipó Range, south-eastern Brazil), and to relate their germination responses to seasonal climatic changes. Samples were exhumed bimonthly and germination was tested under a 12-h photoperiod (30 μmol m− 2s− 1) at optimal germination temperature. The seeds of Comanthera showed high deterioration after the first year of burial, especially C. elegans, which reflects their incapacity to form viable soil seed banks. The buried seeds of C. bisulcata, S. anthemidiflorus and S. verticillatus acquired secondary dormancy during the rainy season (spring/summer, higher temperatures) which was alleviated during the subsequent dry season (autumn/winter, lower temperatures). It is concluded that C. bisulcata, S. anthemidiflorus, and S. verticillatus form seed banks of the persistent type and demonstrate consecutive cycles of germination/dormancy, accompanying annual seasonal changes for at least 2 years.

Germination timing is a key transition of life history. It not only links subsequent life-history traits, such as plant height and flowering time, but also provides a link to the previous generation through the influence of the maternal environment. Environmental factors may mediate these key links, and consequences of this process may influence species regeneration and dispersal. However, little is known about how environmental factors mediate these key links. Here, germination timing under high (natural light) and low light treatments was estimated for 476 angiosperm species of the eastern Tibetan Plateau grasslands. Furthermore, we used standard (std) and phylogenetic (phy) comparative methods to test if germination timing was associated with plant height, flowering time and maternal habitats under both light treatments. Germination timing was positively correlated with plant height only in low light in std-methods. Germination timing was associated with onset of flowering in both light treatments in std-methods, but only in low light when using phy-methods. Germination timing was positively correlated with elevation only in low light when using both comparative methods. Germination timing was correlated with water in maternal habitat only in high light when using both comparative methods. Germination timing was associated with light in maternal habitat in both light treatments in std-methods, but only in high light when using phy-methods. In summary, light-dependent associations of germination timing with subsequent life-history traits and maternal habitats may influence the probability of plant species life-cycle completion and influence distribution and dispersal of plant species in natural plant communities.

Although Asteraceae species are important in the cold deserts of Central Asia, little is known about their seed dormancy and germination. We determined dormancy breaking and germination requirements of three annual Asteraceae, Echinops gmelinii, Epilasia acrolasia and Koelpinia linearis. Achenes (seeds) were tested for germination in light and in darkness over a range of alternating temperatures after various periods of burial outdoors and of dry storage. Germination phenology was monitored for seeds sown in irrigated and non-irrigated sand, and temperature requirements for dormancy break were determined under wet and dry conditions. Effects of pericarp and phyllaries on germination of E. acrolasia and E. gmelinii, respectively, were determined. Low percentages of 20-day-old seeds of E. acrolasia and K. linearis were non-dormant and germinated to low percentages over the range of temperatures, whereas all seeds of E. gmelinii were dormant. As seeds of the three species afterripened, they germinated over the range of temperatures. Whether seeds germinated in autumn or spring depended on the amount of sand moisture. Mechanical resistance of the pericarp and phyllaries reduced germination of E. acrolasia and E. gmelinii, respectively. Temperature requirements for germination as seeds come out of dormancy do not correspond to any of the known five types of non-deep physiological dormancy (PD). Thus, a sixth type is recognized in which germination occurs over the same range of temperatures in the early and late stages of dormancy break. Type 6 allows seeds to germinate at high or at low temperatures, whenever sand moisture is non-limiting.

Soybean seeds are prone to flooding injury just after planting if they are exposed to excess moisture. We investigated the flooding tolerance of soybean seeds to clarify the relationship between flooding injury and imbibition, to identify factors that could provide fundamental information for the breeding of flooding-tolerant cultivars. Seven cultivars were used for this study. The seeds were geminated in a paper towel after a flooding treatment and then evaluated for survival. The imbibition of submerged seeds (passive imbibition) was evaluated as the seed fresh weight change during the flooding process. The imbibition of seeds with capillary effect (capillary imbibition) was measured by the bottom water supply method. Furthermore, the conductivity of the seed coat and seed osmolarity were measured. After 3 h of flooding, significant differences in survival were detected among cultivars. In addition, the passive imbibition during 10–30 min of flooding, and the capillary imbibition during 0–10 min of flooding were caused by significant differences in the imbibition rate among cultivars. Although neither imbibition showed a significant correlation with the survival directly, the ratio between the passive and the capillary imbibition rate was significantly correlated with survival. Factors affecting imbibition included the hydraulic conductivity of the seed coat and seed osmolarity, which were significantly correlated with the passive and the capillary imbibition rate, respectively. Thus, the balance between the capillary and passive imbibition behaviour of seeds, affected by the hydraulic conductivity of the seed coat and seed osmolarity, was closely correlated with the occurrence of flooding injury in soybean seeds.

Theoretical models predict that seed size and seed-bank persistence evolve interdependently, such that strong selection for one trait corresponds with weak selection for the other. This framework has been supported and rejected by empirical data, and thus, conclusive evidence is lacking. We expanded the seed size–persistence framework to include seed-coat thickness, a defence trait previously correlated with seed survival in soil. To do this, we used Abutilon theophrasti accessions with varied evolutionary histories and we quantified associations among seed traits including morphology, size, coat thickness, dormancy (percentage of viable seeds that fail to germinate under optimum conditions) and seed-bank persistence (percentage of viable seeds remaining after 1 year of burial). Statistical models were developed to test the hypothesis that combined measurements of seed-coat thickness and seed size better explain variability in seed-bank persistence than seed-size data alone. Results indicated that measurements of seed size (length, width, mass) were negatively correlated with coat:width ratio (coat thickness relative to seed width) and coat:mass ratio (coat thickness relative to seed mass). Accessions characterized by smaller seeds with proportionally thicker seed coats were more dormant and more persistent in soil than accessions characterized by larger seeds with proportionally thinner seed coats. Seed-coat thickness data improved the explanatory power of logistic regression models for seed-size effects on both seed-bank persistence and dormancy. These results indicate that supplementing seed-size data with seed-defence data may clarify previously reported contradictory results regarding trade-offs between seed size and seed-bank persistence.

The soil seed bank is the reserve of viable seeds found in the soil. This reserve contributes to plant population persistence in unpredictable environments; thus, determining its presence is basic to understanding recruitment patterns and population dynamics. Studies of soil seed banks in the Cactaceae are scarce, although these plants are ecologically dominant in American arid and semi-arid environments. Most studies have inferred the presence of seed banks by analysing morphological seed traits or germination of seeds stored in the laboratory for different periods of time. Few studies have determined their presence through evaluation of distribution, density and longevity of seeds in the field. To fill this information gap, we determined the existence of, and studied, the soil seed bank of Stenocereus stellatus, a columnar cactus endemic to central Mexico. This study reports the evaluation of these characteristics in the field and discusses whether this species forms a soil seed bank. We found a higher number of seeds under shrubs than in areas lacking vegetation. Recently dispersed seeds did not germinate because they have primary dormancy. This dormancy was broken after 6 months of burial in the soil. Seeds buried for 10 months entered secondary dormancy and they were not viable at 24 months, probably because of pathogen attack. Considering dormancy and seed longevity, we suggest that S. stellatus has the potential to form a short-term persistent seed bank. However, this should be confirmed by conducting studies on other S. stellatus populations throughout their geographical distribution.

Many temperate plant genera, like Sambucus, have species with range disjunctions among North America, Europe and/or Asia. Cold stratification (sometimes in combination with warm stratification) is the primary mechanism to break seed dormancy in these species. For some of these genera showing Northern Hemispheric disjunctions, members also occur in subtropical or tropical regions, mostly confined to higher elevations where climate and vegetation differ from those in northern latitudes. We made two hypotheses concerning germination for the subtropical Taiwanese Sambucus chinensis: (1) seeds from populations exposed to warm temperatures would require warm stratification, and (2) seeds from populations exposed to cold temperatures need cold stratification. We investigated the germination (including embryo growth) of non-stratified seeds over a range of temperatures and tested the effects of cold stratification and of gibberellins GA3 and GA4 on germination. The amount and timing of germination among populations varied substantially in response to temperature treatments. Seeds from all populations of this species required warm temperatures for dormancy break and germination, regardless of environmental conditions. As such, the majority of seeds had non-deep simple morphophysiological dormancy, which, until now, has not been reported in any members of Sambucus. The seed characteristics of the subtropical S. chinensis are different from those of temperate members of the genus in which cold stratification is the predominate treatment to overcome dormancy.

Floodplain meadow ecosystems are characterized by high water level fluctuations and highly variable soil water potentials. Additionally, climate change scenarios indicate an increasing risk for summer drought along the northern Upper Rhine and the Middle Elbe River, Germany. While adult plants often persist even after strong changes in water availability, early life phases, such as seed germination and seedling establishment, might be more vulnerable. Therefore we tested whether reduced soil water potentials will affect the germination of meadow species and whether the response varies between (1) forbs indicative of wet and dry habitats and (2) seeds originating from sites along the rivers Elbe and Rhine. We exposed seeds of 20 floodplain meadow species with different moisture requirements from five plant families to a water potential gradient ranging from 0 to − 1.5 MPa. While across species germination percentage and synchrony decreased, germination time increased at reduced water potentials. Germination of the species indicative of dry habitats decreased more strongly, was slower and less synchronous at reduced water potentials than that of species indicative of wet habitats. Seeds from sites along the rivers Elbe and Rhine did not differ in their germination characteristics. We propose that species of wet sites follow an all-or-nothing-strategy with fast and synchronous germination to maximize competitive advantages, betting on a high probability of moist conditions for establishment (optimists). In contrast, species from dry sites appear to follow a bet-hedging strategy with a moisture-sensing mechanism for unsuitable conditions (pessimists), resulting in a slower and less synchronous germination.